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3D initial conditions in Gray-Scott
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@brownbaerchen
brownbaerchen committed Nov 16, 2024
1 parent 1196767 commit c275e02
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Showing 3 changed files with 54 additions and 23 deletions.
13 changes: 7 additions & 6 deletions pySDC/implementations/problem_classes/GrayScott_MPIFFT.py
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Original file line number Diff line number Diff line change
Expand Up @@ -200,7 +200,6 @@ def u_exact(self, t, seed=10700000):
Exact solution.
"""
assert t == 0.0, 'Exact solution only valid as initial condition'
assert self.ndim == 2, 'The initial conditions are 2D for now..'

xp = self.xp

Expand All @@ -222,12 +221,13 @@ def u_exact(self, t, seed=10700000):
_v[...] = xp.sqrt(F) * (A + xp.sqrt(A**2 - 4)) / 2

for _ in range(-self.num_blobs):
x0, y0 = rng.random(size=2) * self.L[0] - self.L[0] / 2
lx, ly = rng.random(size=2) * self.L[0] / self.nvars[0] * 30
x0 = rng.random(size=self.ndim) * self.L[0] - self.L[0] / 2
l = rng.random(size=self.ndim) * self.L[0] / self.nvars[0] * 30

mask_x = xp.logical_and(self.X[0] > x0, self.X[0] < x0 + lx)
mask_y = xp.logical_and(self.X[1] > y0, self.X[1] < y0 + ly)
mask = xp.logical_and(mask_x, mask_y)
masks = [xp.logical_and(self.X[i] > x0[i], self.X[i] < x0[i] + l[i]) for i in range(self.ndim)]
mask = masks[0]
for m in masks[1:]:
mask = xp.logical_and(mask, m)

_u[mask] = rng.random()
_v[mask] = rng.random()
Expand All @@ -236,6 +236,7 @@ def u_exact(self, t, seed=10700000):
"""
Blobs as in https://www.chebfun.org/examples/pde/GrayScott.html
"""
assert self.ndim == 2, 'The initial conditions are 2D for now..'

inc = self.L[0] / (self.num_blobs + 1)

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1 change: 1 addition & 0 deletions pySDC/implementations/problem_classes/generic_MPIFFT_Laplacian.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,7 @@ class IMEX_Laplacian_MPIFFT(Problem):
r"""
Generic base class for IMEX problems using a spectral method to solve the Laplacian implicitly and a possible rest
explicitly. The FFTs are done with``mpi4py-fft`` [1]_.
Works in two and three dimensions.
Parameters
----------
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63 changes: 46 additions & 17 deletions pySDC/projects/GPU/configs/GS_configs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,7 @@ class GrayScott(Config):
num_frames = 200
sweeper_type = 'IMEX'
res_per_blob = 2**7
ndim = 3

def get_LogToFile(self, ranks=None):
import numpy as np
Expand All @@ -49,16 +50,14 @@ def process_solution(L):
't': L.time + L.dt,
'u': uend[0].get().view(np.ndarray),
'v': uend[1].get().view(np.ndarray),
'X': L.prob.X[0].get().view(np.ndarray),
'Y': L.prob.X[1].get().view(np.ndarray),
'X': L.prob.X.get().view(np.ndarray),
}
else:
return {
't': L.time + L.dt,
'u': uend[0],
'v': uend[1],
'X': L.prob.X[0],
'Y': L.prob.X[1],
'X': L.prob.X,
}

def logging_condition(L):
Expand All @@ -75,7 +74,7 @@ def logging_condition(L):
LogToFile.logging_condition = logging_condition
return LogToFile

def plot(self, P, idx, n_procs_list): # pragma: no cover
def plot(self, P, idx, n_procs_list, projection='xy'): # pragma: no cover
import numpy as np
from matplotlib import ticker as tkr

Expand All @@ -99,19 +98,49 @@ def plot(self, P, idx, n_procs_list): # pragma: no cover
vmax['u'] = max([vmax['u'], buffer[f'u-{rank}']['u'].real.max()])

for rank in range(n_procs_list[2]):
im = ax.pcolormesh(
buffer[f'u-{rank}']['X'],
buffer[f'u-{rank}']['Y'],
buffer[f'u-{rank}']['v'].real,
vmin=vmin['v'],
vmax=vmax['v'],
cmap='binary',
)
if len(buffer[f'u-{rank}']['X']) == 2:
ax.set_xlabel('$x$')
ax.set_ylabel('$y$')
im = ax.pcolormesh(
buffer[f'u-{rank}']['X'][0],
buffer[f'u-{rank}']['X'][1],
buffer[f'u-{rank}']['v'].real,
vmin=vmin['v'],
vmax=vmax['v'],
cmap='binary',
)
else:
v3d = buffer[f'u-{rank}']['v'].real

if projection == 'xy':
slices = [slice(None), slice(None), v3d.shape[2] // 2]
x = buffer[f'u-{rank}']['X'][0][*slices]
y = buffer[f'u-{rank}']['X'][1][*slices]
ax.set_xlabel('$x$')
ax.set_ylabel('$y$')
elif projection == 'xz':
slices = [slice(None), v3d.shape[1] // 2, slice(None)]
x = buffer[f'u-{rank}']['X'][0][*slices]
y = buffer[f'u-{rank}']['X'][2][*slices]
ax.set_xlabel('$x$')
ax.set_ylabel('$z$')
elif projection == 'yz':
slices = [v3d.shape[0] // 2, slice(None), slice(None)]
x = buffer[f'u-{rank}']['X'][1][*slices]
y = buffer[f'u-{rank}']['X'][2][*slices]
ax.set_xlabel('$y$')
ax.set_ylabel('$z$')

im = ax.pcolormesh(
x,
y,
v3d[*slices],
vmin=vmin['v'],
vmax=vmax['v'],
cmap='binary',
)
fig.colorbar(im, cax, format=tkr.FormatStrFormatter('%.1f'))
ax.set_title(f't={buffer[f"u-{rank}"]["t"]:.2f}')
ax.set_xlabel('$x$')
ax.set_ylabel('$y$')
ax.set_aspect(1.0)
ax.set_aspect(1.0)
return fig

Expand All @@ -130,7 +159,7 @@ def get_description(self, *args, res=-1, **kwargs):
desc['sweeper_params']['QI'] = 'MIN-SR-S'
desc['sweeper_params']['QE'] = 'PIC'

desc['problem_params']['nvars'] = (2**8 if res == -1 else res,) * 2
desc['problem_params']['nvars'] = (2**8 if res == -1 else res,) * self.ndim
desc['problem_params']['Du'] = 0.00002
desc['problem_params']['Dv'] = 0.00001
desc['problem_params']['A'] = 0.04
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